Geonosis & Kamino are Republic Vs. Seperatists only.
Endor & Hoth are Empire Vs. Rebels only.
The rest of the maps you can choose your factions, but the Empire always fights the Rebels and the Republic always fight the Seperatists. You cannot (unfortunately) mix and match.
Each faction has their version of a pilot, but anyone can fly a vehicle. Pilots just slowly heal the vehicles they are inside.